Climate-related naturally occurring epimutation and their roles in plant adaptation in A. thaliana.

DNA methylation has been proposed to be an important mechanism that allows plants to respond to their environments sometimes entirely uncoupled from genetic variation. To understand the genetic basis, biological functions and climatic relationships of DNA methylation at a population scale in Arabidopsis thaliana, we performed a genome-wide association analysis with high-quality single nucleotide polymorphisms (SNPs), and found that ~56% on average, especially in the CHH sequence context (71%), of the differentially methylated regions (DMRs) are not tagged by SNPs. Among them, a total of 3235 DMRs are significantly associated with gene expressions and potentially heritable. 655 of the 3235 DMRs are associated with climatic variables, and we experimentally verified one of them, HEI10 (HUMAN ENHANCER OF CELL INVASION NO.10). Such epigenetic loci could be subjected to natural selection thereby affecting plant adaptation, and would be expected to be an indicator of accessions at risk. We therefore incorporated these climate-related DMRs into a gradient forest model, and found that the natural A. thaliana accessions in Southern Europe that may be most at risk under future climate change. Our findings highlight the importance of integrating DNA methylation that is independent of genetic variations, and climatic data to predict plants' vulnerability to future climate change.

Hepatic transcriptome profiling of largemouth bass (Micropterus salmoides Lacépède) injected with Flavobacterium covae or lipopolysaccharide.

Flavobacterium covae (columnaris) is the most detrimental bacterial disease affecting the largemouth bass (Micropterus salmoides Lacépède) aquaculture industry. In the current study, fish received an intraperitoneal injection of either 1× PBS (100 µL), LPS in PBS (100 µL, 10 µg/mL), or F. covae (100 µL, 2.85 × 1011 CFU/mL) to simulate immunological challenges. After 24 h post-injection, liver tissue from the control and treated groups were then collected for transcriptome analysis. Results of the Gene Ontology (GO) and KEGG pathway analyses for the F. covae and LPS-injected groups found differentially expressed genes (DEGs) enriched primarily in toll-like receptors (TLRs), cytokine-cytokine receptors, complement and coagulation cascades, and the PPAR signalling pathways. This suggests that the liver immune system is enhanced by these five combined pathways. Additionally, the DEGs TLR5, MYD88, and IL-1 were significantly upregulated in F. covae and LPS-injected fish compared to the controls, whereas IL-8 was downregulated. The upregulation of TLR5 was unexpected as F. covae lacks flagellin, the protein that binds to TLR5. Additionally, it is unknown whether the TLR5 is upregulated by LPS. Further research into the upregulation of TLR5 is warranted. These results provide insight into immune responses and associated pathways contributing to the immune system in the liver during columnaris infection and induced response to LPS in largemouth bass.

SarCTAB: an efficient and cost-effective DNA isolation protocol from geophytes.

Geophytes are herbaceous plants that grow anew from underground buds and are excellent models to study storage organ formation. However, molecular studies involving geophytes are constrained due to the presence of a wide spectrum of polysaccharides and polyphenols that contaminate the genomic DNA. At present, several protocols exist for the extraction of genomic DNA from different plant species; however, isolating high-quality DNA from geophytes is challenging. Such challenges are further complexed by longer incubation time and multiple precipitation steps involved in existing DNA isolation methods. To overcome such problems, we aimed to establish a DNA extraction method (SarCTAB) which is an economical, quick, and sustainable way of DNA isolation from geophytes. We improved the traditional CTAB method by optimizing key ingredients such as sarcosine, ß-mercaptoethanol, and high molar concentration of sodium chloride (NaCl), which resulted in high concentration and good-quality DNA with lesser polysaccharides, proteins, and polyphenols. This method was evaluated to extract DNA from storage organs of six different geophytes. The SarCTAB method provides an average yield of 1755 ng/µl of high-quality DNA from 100 mg of underground storage tissues with an average standard purity of 1.86 (260/280) and 1.42 (260/230). The isolated genomic DNA performed well with Inter-simple sequence repeat (ISSR) amplification, restriction digestion with EcoRI, and PCR amplification of plant barcode genes viz. matK and rbcL. Also, the cost involved in DNA isolation was low when compared to that with commercially available kits. Overall, SarCTAB method works effectively to isolate high-quality genomic DNA in a cost-effective manner from the underground storage tissues of geophytes, and can be applied for next-generation sequencing, DNA barcoding, and whole genome bisulfite sequencing.

Himalayan moss Takakia: a tale of its evolution, adaptation, and climate crisis.

Plants thriving in harsh environments are at risk of extinction due to climate change. Hu et al. sequenced the genome of a high-altitude Himalayan moss, Takakia lepidozioides, and revealed that genes contributing to growth and stress adaptation are fast-evolving. However, the population of Takakia is now declining, inferring early warning signals of global warming.

Genome-wide identification and expression analysis reveal the role of histone methyltransferase and demethylase genes in heat stress response in potato (Solanum tuberosum L.).

BACKGROUND: Potato (Solanum tuberosum L.), the third most important non-cereal crop, is sensitive to high temperature. Histone modifications have been known to regulate various abiotic stress responses. However, the role of histone methyltransferases and demethylases remain unexplored in potato under heat stress. METHODS: Potato genome database was used for genome-wide analysis of StPRMT and StHDMA gene families, which were further characterized by analyzing gene structure, conserved motif, domain organization, sub-cellular localization, promoter region and phylogenetic relationships. Additionally, expression profiling under high-temperature stress in leaf and stolon tissue of heat contrasting potato genotypes was done to study their role in response to high temperature stress. RESULTS: The genome-wide analysis led to identification of nine StPRMT and eleven StHDMA genes. Structural analysis, including conserved motifs, exon/intron structure and phylogenetic relationships classified StPRMT and StHDMA gene families into two classes viz. Class I and Class II. A variety of cis-regulatory elements were explored in the promoter region associated with light, developmental, hormonal and stress responses. Prediction of sub-cellular localization of StPRMT proteins revealed their occurrence in nucleus and cytoplasm, whereas StHDMA proteins were observed in different sub-cellular compartments. Furthermore, expression profiling of StPRMT and StHDMA gene family members revealed genes responding to heat stress. Heat-inducible expression of StPRMT1, StPRMT3, StPRMT4 and StPRMT5 in leaf and stolon tissues of HS and HT cultivar indicated them as probable candidates for enhancing thermotolerance in potato. However, StHDMAs responded dynamically in leaf and stolon tissue of heat contrasting genotypes under high temperature. CONCLUSION: The current study presents a detailed analysis of histone modifiers in potato and indicates their role as an important epigenetic regulators modulating heat tolerance. GENERAL SIGNIFICANCE: Understanding epigenetic mechanisms underlying heat tolerance in potato will contribute towards breeding of thermotolerant potato varieties.

Genetic resources and breeding approaches for improvement of amaranth (Amaranthus spp.) and quinoa (Chenopodium quinoa).

Nowadays, the human population is more concerned about their diet and very specific in choosing their food sources to ensure a healthy lifestyle and avoid diseases. So people are shifting to more smart nutritious food choices other than regular cereals and staple foods they have been eating for a long time. Pseudocereals, especially, amaranth and quinoa, are important alternatives to traditional cereals due to comparatively higher nutrition, essential minerals, amino acids, and zero gluten. Both Amaranchaceae crops are low-input demanding and hardy plants tolerant to stress, drought, and salinity conditions. Thus, these crops may benefit developing countries that follow subsistence agriculture and have limited farming resources. However, these are underutilized orphan crops, and the efforts to improve them by reducing their saponin content remain ignored for a long time. Furthermore, these crops have very rich variability, but the progress of their genetic gain for getting high-yielding genotypes is slow. Realizing problems in traditional cereals and opting for crop diversification to tackle climate change, research should be focused on the genetic improvement for low saponin, nutritionally rich, tolerant to biotic and abiotic stresses, location-specific photoperiod, and high yielding varietal development of amaranth and quinoa to expand their commercial cultivation. The latest technologies that can accelerate the breeding to improve yield and quality in these crops are much behind and slower than the already established major crops of the world. We could learn from past mistakes and utilize the latest trends such as CRISPR/Cas, TILLING, and RNA interference (RNAi) technology to improve these pseudocereals genetically. Hence, the study reviewed important nutrition quality traits, morphological descriptors, their breeding behavior, available genetic resources, and breeding approaches for these crops to shed light on future breeding strategies to develop superior genotypes.

Functional divergence of Heat Shock Factors (Hsfs) during heat stress and recovery at the tissue and developmental scales in C4 grain amaranth (Amaranthus hypochondriacus).

Two major future challenges are an increase in global earth temperature and a growing world population, which threaten agricultural productivity and nutritional food security. Underutilized crops have the potential to become future climate crops due to their high climate-resilience and nutritional quality. In this context, C4 pseudocereals such as grain amaranths are very important as C4 crops are more heat tolerant than C3 crops. However, the thermal sensitivity of grain amaranths remains unexplored. Here, Amaranthus hypochondriacus was exposed to heat stress at the vegetative and reproductive stages to capture heat stress and recovery responses. Heat Shock Factors (Hsfs) form the central module to impart heat tolerance, thus we sought to identify and characterize Hsf genes. Chlorophyll content and chlorophyll fluorescence (Fv/Fm) reduced significantly during heat stress, while malondialdehyde (MDA) content increased, suggesting that heat exposure caused stress in the plants. The genome-wide analysis led to the identification of thirteen AhHsfs, which were classified into A, B and C classes. Gene expression profiling at the tissue and developmental scales resolution under heat stress revealed the transient upregulation of most of the Hsfs in the leaf and inflorescence tissues, which reverted back to control levels at the recovery time point. However, a few Hsfs somewhat sustained their upregulation during recovery phase. The study reported the identification, physical location, gene/motif structure, promoter analysis and phylogenetic relationships of Hsfs in Amaranthus hypochondriacus. Also, the genes identified may be crucial for future gene functional studies and develop thermotolerant cultivars.

Thermosensitivity of pollen: a molecular perspective.

A current trend in climate comprises adverse weather anomalies with more frequent and intense temperature events. Heatwaves are a serious threat to global food security because of the susceptibility of crop plants to high temperatures. Among various developmental stages of plants, even a slight rise in temperature during reproductive development proves detrimental, thus making sexual reproduction heat vulnerable. In this context, male gametophyte or pollen development stages are the most sensitive ones. High-temperature exposure induces pollen abortion, reducing pollen viability and germination rate with a concomitant effect on seed yield. This review summarizes the ultrastructural, morphological, biochemical, and molecular changes underpinning high temperature-induced aberrations in male gametophytes. Specifically, we highlight the temperature sensing cascade operating in pollen, involving reactive oxygen species (ROS), heat shock factors (HSFs), a hormones and transcriptional regulatory network. We also emphasize integrating various omics approaches to decipher the molecular events triggered by heat stress in pollen. The knowledge of genes, proteins, and metabolites conferring thermotolerance in reproductive tissues can be utilized to breed/engineer thermotolerant crops to ensure food security.

Nocardiopsis lucentensis and thiourea co-application mitigates arsenic stress through enhanced antioxidant metabolism and lignin accumulation in rice.

Arsenic (As) is a group-1 carcinogenic metalloid that threatens global food safety and security, primarily via its phytotoxicity in the staple crop rice. In the present study, ThioAC, the co-application of thiourea (TU, a non-physiological redox regulator) and N. lucentensis (Act, an As-detoxifying actinobacteria), was evaluated as a low-cost approach for alleviating As(III) toxicity in rice. To this end, we phenotyped rice seedlings subjected to 400 mg kg-1 As(III) with/without TU, Act or ThioAC and analyzed their redox status. Under As-stress conditions, ThioAC treatment stabilized photosynthetic performance, as indicated by 78 % higher total chlorophyll accumulation and 81 % higher leaf biomass, compared with those of As-stressed plants. Further, ThioAC improved root lignin levels (2.08-fold) by activating the key enzymes of lignin biosynthesis under As-stress. The extent of reduction in total As under ThioAC (36 %) was significantly higher than TU (26 %) and Act (12 %), compared to those of As-alone treatment, indicating their synergistic interaction. The supplementation of TU and Act activated enzymatic and non-enzymatic antioxidant systems, respectively, with a preference for young (TU) and old (Act) leaves. Additionally, ThioAC activated enzymatic antioxidants, specifically GR (∼3-fold), in a leaf-age specific manner and suppressed ROS-producing enzymes to near-control levels. This coincided with 2-fold higher induction of polyphenols and metallothionins in ThioAC-supplemented plants, resulting in improved antioxidant defence against As-stress. Thus, our findings highlighted ThioAC application as a robust, cost-effective ameliorative strategy, for achieving As-stress mitigation in a sustainable manner.

Elevated CO2 mitigates the impact of drought stress by upregulating glucosinolate metabolism in Arabidopsis thaliana.

Elevated CO2 (eCO2 ) reduces the impact of drought, but the mechanisms underlying this effect remain unclear. Therefore, we used a multidisciplinary approach to investigate the interaction of drought and eCO2 in Arabidopsis thaliana leaves. Transcriptome and subsequent metabolite analyses identified a strong induction of the aliphatic glucosinolate (GL) biosynthesis as a main effect of eCO2 in drought-stressed leaves. Transcriptome results highlighted the upregulation of ABI5 and downregulation of WRKY63 transcription factors (TF), known to enhance and inhibit the expression of genes regulating aliphatic GL biosynthesis (e.g., MYB28 and 29 TFs), respectively. In addition, eCO2 positively regulated aliphatic GL biosynthesis by MYB28/29 and increasing the accumulation of GL precursors. To test the role of GLs in the stress-mitigating effect of eCO2 , we investigated the effect of genetic perturbations of the GL biosynthesis. Overexpression of MYB28, 29 and 76 improved drought tolerance by inducing stomatal closure and maintaining plant turgor, whereas loss of cyp79f genes reduced the stress-mitigating effect of eCO2 and decreased drought tolerance. Overall, the crucial role of GL metabolism in drought stress mitigation by eCO2 could be a beneficial trait to overcome future climate challenges.

The interplay of DNA methyltransferases and demethylases with tuberization genes in potato (Solanum tuberosum L.) genotypes under high temperature.

Potato is a temperate crop consumed globally as a staple food. High temperature negatively impacts the tuberization process, eventually affecting crop yield. DNA methylation plays an important role in various developmental and physiological processes in plants. It is a conserved epigenetic mark determined by the dynamic concurrent action of cytosine-5 DNA methyltransferases (C5-MTases) and demethylases (DeMets). However, C5-MTases and DeMets remain unidentified in potato, and their expression patterns are unknown under high temperatures. Here, we performed genome-wide analysis and identified 10 C5-MTases and 8 DeMets in potatoes. Analysis of their conserved motifs, gene structures, and phylogenetic analysis grouped C5-MTases into four subfamilies (StMET, StCMT3, StDRM, and StDNMT2) and DeMets into three subfamilies (StROS, StDML, and StDME). Promoter analysis showed the presence of multiple cis-regulatory elements involved in plant development, hormone, and stress response. Furthermore, expression dynamics of C5-MTases and DeMets were determined in the different tissues (leaf, flower, and stolon) of heat-sensitive (HS) and heat-tolerant (HT) genotypes under high temperature. qPCR results revealed that high temperature resulted in pronounced upregulation of CMT and DRM genes in the HT genotype. Likewise, demethylases showed strong upregulation in HT genotype as compared to HS genotype. Several positive (StSP6A and StBEL5) and negative (StSP5G, StSUT4, and StRAP1) regulators are involved in the potato tuberization. Expression analysis of these genes revealed that high temperature induces the expression of positive regulators in the leaf and stolon samples of HT genotype, possibly through active DNA demethylation and RNA-directed DNA methylation (RdDM) pathway components. Our findings lay a framework for understanding how epigenetic pathways synergistically or antagonistically regulate the tuberization process under high-temperature stress in potatoes. Uncovering such mechanisms will contribute to potato breeding for developing thermotolerant potato varieties.

Cold adaptation strategies in plants-An emerging role of epigenetics and antifreeze proteins to engineer cold resilient plants.

Cold stress adversely affects plant growth, development, and yield. Also, the spatial and geographical distribution of plant species is influenced by low temperatures. Cold stress includes chilling and/or freezing temperatures, which trigger entirely different plant responses. Freezing tolerance is acquired via the cold acclimation process, which involves prior exposure to non-lethal low temperatures followed by profound alterations in cell membrane rigidity, transcriptome, compatible solutes, pigments and cold-responsive proteins such as antifreeze proteins. Moreover, epigenetic mechanisms such as DNA methylation, histone modifications, chromatin dynamics and small non-coding RNAs play a crucial role in cold stress adaptation. Here, we provide a recent update on cold-induced signaling and regulatory mechanisms. Emphasis is given to the role of epigenetic mechanisms and antifreeze proteins in imparting cold stress tolerance in plants. Lastly, we discuss genetic manipulation strategies to improve cold tolerance and develop cold-resistant plants.

Multifaceted roles of GRAS transcription factors in growth and stress responses in plants.

The GAI-RGA- and -SCR (GRAS) proteins regulate a myriad of biological functions in plants. The C-terminus of GRAS proteins is highly conserved, whereas the N-terminus is hypervariable. So far, GRAS proteins have been reported in more than 50 plant species. However, not many GRAS proteins are characterized, thus limiting the revelation of their many functions. This review provides a recent update on GRAS proteins, including their structural features, evolutionary gene family expansion/diversification, and interacting protein partners. Also, a mechanistic insight on GRAS protein-mediated plant growth and abiotic stress response is provided. For this, we assessed the transcriptional dynamics of GRAS genes in rice (monocot) and Arabidopsis (dicot) at different developmental stages and under several abiotic stresses. Lastly, the usage of genome-editing tools such as the CRISPR/Cas9 system to understand GRAS molecular functions is highlighted, with the ultimate goal of developing improved agronomic and climate-resilient traits in plants.

Emerging Roles of SWEET Sugar Transporters in Plant Development and Abiotic Stress Responses.

Sugars are the major source of energy in living organisms and play important roles in osmotic regulation, cell signaling and energy storage. SWEETs (Sugars Will Eventually be Exported Transporters) are the most recent family of sugar transporters that function as uniporters, facilitating the diffusion of sugar molecules across cell membranes. In plants, SWEETs play roles in multiple physiological processes including phloem loading, senescence, pollen nutrition, grain filling, nectar secretion, abiotic (drought, heat, cold, and salinity) and biotic stress regulation. In this review, we summarized the role of SWEET transporters in plant development and abiotic stress. The gene expression dynamics of various SWEET transporters under various abiotic stresses in different plant species are also discussed. Finally, we discuss the utilization of genome editing tools (TALENs and CRISPR/Cas9) to engineer SWEET genes that can facilitate trait improvement. Overall, recent advancements on SWEETs are highlighted, which could be used for crop trait improvement and abiotic stress tolerance.

Salinity responses and tolerance mechanisms in underground vegetable crops: an integrative review.

MAIN CONCLUSION: The present review gives an insight into the salinity stress tolerance responses and mechanisms of underground vegetable crops. Phytoprotectants, agronomic practices, biofertilizers, and modern biotechnological approaches are crucial for salinity stress management. Underground vegetables are the source of healthy carbohydrates, resistant starch, antioxidants, vitamins, mineral, and nutrients which benefit human health. Soil salinity is a serious threat to agriculture that severely affects the growth, development, and productivity of underground vegetable crops. Salt stress induces several morphological, anatomical, physiological, and biochemical changes in crop plants which include reduction in plant height, leaf area, and biomass. Also, salinity stress impedes the growth of the underground organs, which ultimately reduces crop yield. Moreover, salt stress is detrimental to photosynthesis, membrane integrity, nutrient balance, and leaf water content. Salt tolerance mechanisms involve a complex interplay of several genes, transcription factors, and proteins that are involved in the salinity tolerance mechanism in underground crops. Besides, a coordinated interaction between several phytoprotectants, phytohormones, antioxidants, and microbes is needed. So far, a comprehensive review of salinity tolerance responses and mechanisms in underground vegetables is not available. This review aims to provide a comprehensive view of salt stress effects on underground vegetable crops at different levels of biological organization and discuss the underlying salt tolerance mechanisms. Also, the role of multi-omics in dissecting gene and protein regulatory networks involved in salt tolerance mechanisms is highlighted, which can potentially help in breeding salt-tolerant underground vegetable crops.

Physiological and molecular insights on wheat responses to heat stress.

Increasing temperature is a key component of global climate change, affecting crop growth and productivity worldwide. Wheat is a major cereal crop grown in various parts of the globe, which is affected severely by heat stress. The morphological parameters affected include germination, seedling establishment, source-sink activity, leaf area, shoot and root growth. The physiological parameters such as photosynthesis, respiration, leaf senescence, water and nutrient relation are also affected by heat. At the cellular level, heat stress leads to the generation of reactive oxygen species that disrupt the membrane system of thylakoid, chloroplast and plasma membrane. The deactivation of the photosystem, reduction in photosynthesis and inactivation of rubisco affect the production of photoassimilates and their allocation. This ultimately affects anthesis, grain filling, size, number and maturity of wheat grains, which hamper crop productivity. The interplay of various systems comprising antioxidants and hormones plays a crucial role in imparting heat stress tolerance in wheat. Thus, implementation of various omics technologies could foster in-depth insights on heat stress effects, eventually devising heat stress mitigation strategies by conventional and modern breeding to develop heat-tolerant wheat varieties. This review provides an integrative view of heat stress responses in wheat and also discusses approaches to develop heat-tolerant wheat varieties.

Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability.

The CMT2 and RNA-directed DNA methylation (RdDM) pathways have been proposed to separately maintain CHH methylation in specific regions of the Arabidopsis thaliana genome. Here, we show that dysfunction of the chromatin remodeler DDM1 causes hundreds of genomic regions to switch from CMT2 dependency to RdDM dependency in DNA methylation. These converted loci are enriched at the edge regions of long transposable elements (TEs). Furthermore, we found that dysfunction in both DDM1 and RdDM causes strong reactivation of TEs and a burst of TE transposition in the first generation of mutant plants, indicating that the DDM1 and RdDM pathways together are critical to maintaining TE repression and protecting genomic stability. Our findings reveal the existence of a pathway conversion-based backup mechanism to guarantee the maintenance of DNA methylation and genome integrity.

An actinomycete strain of Nocardiopsis lucentensis reduces arsenic toxicity in barley and maize.

Accumulation of arsenic in plant tissues poses a substantial threat to global crop yields. The use of plant growth-promoting bacterial strains to mitigate heavy metal toxicity has been illustrated before. However, its potential to reduce plant arsenic uptake and toxicity has not been investigated to date. Here, we describe the identification and characterization of a Nocardiopsis lucentensis strain isolated from heavy metal contaminated soil. Inoculation with this bioactive actinomycete strain decreased arsenic root and shoot bioaccumulation in both C3 and C4 crop species namely barley and maize. Upon arsenate treatment, N. lucentensis S5 stimulated root citric acid production and the plant's innate detoxification capacity in a species-specific manner. In addition, this specific strain promoted biomass gain, despite substantial tissue arsenic levels. Detoxification (metallothionein, phytochelatin, glutathione-S-transferase levels) was upregulated in arsenate-exposed shoot and roots, and this response was further enhanced upon S5 supplementation, particularly in barley and maize roots. Compared to barley, maize plants were more tolerant to arsenate-induced oxidative stress (less H2O2 and lipid peroxidation levels). However, barley plants invested more in antioxidative capacity induction (ascorbate-glutathione turnover) to mitigate arsenic oxidative stress, which was strongly enhanced by S5. We quantify and mechanistically discuss the physiological and biochemical basis of N. lucentensis-mediated plant biomass recovery on arsenate polluted soils. Our findings substantiate the potential applicability of a bactoremediation strategy to mitigate arsenic-induced yield loss in crops.

Soil arsenic toxicity differentially impacts C3 (barley) and C4 (maize) crops under future climate atmospheric CO2.

Soil arsenic (As) contamination limits global agricultural productivity. Anthropogenic emissions are causing atmospheric CO2 levels to rise. Elevated CO2 (eCO2) boosts plant growth both under optimal and suboptimal growth conditions. However, the crop-specific interaction between eCO2 and soil arsenic exposure has not been investigated at the whole plant, physiological and biochemical level. Here, we tested the effects of eCO2 (620 ppm) and soil As exposure (mild and severe treatments, 25 and 100 mg As/Kg soil) on growth, photosynthesis and redox homeostasis in barley (C3) and maize (C4). Compared to maize, barley was more susceptible to soil As exposure at ambient CO2 levels. Barley plants accumulated more As, particularly in roots. As accumulation inhibited plant growth and induced oxidative damage in a species-specific manner. As-exposed barley experienced severe oxidative stress as illustrated by high H2O2 and protein oxidation levels. Interestingly, eCO2 differentially mitigated As-induced stress in barley and maize. In barley, eCO2 exposure reduced photorespiration, H2O2 production, and lipid/protein oxidation. In maize eCO2 exposure led to an upregulation of the ascorbate-glutathione (ASC/GSH)-mediated antioxidative defense system. Combined, this work highlights how ambient and future eCO2 levels differentially affect the growth, physiology and biochemistry of barley and maize crops exposed to soil As pollution.

CRISPR/Cas9-Based Genome Editing Toolbox for Arabidopsis thaliana.

CRISPR/Cas9 system has emerged as a powerful genome engineering tool to study gene function and improve plant traits. Genome editing is achieved at a specific genome sequence by Cas9 endonuclease to generate double standard breaks (DSBs) directed by short guide RNAs (sgRNAs). The DSB is repaired by error-prone nonhomologous end joining (NHEJ) or error-free homology-directed repair (HDR) pathways, resulting in gene mutation or sequence replacement, respectively. These cellular DSB repair pathways can be exploited to knock out or replace genes. Also, cytidine or adenine base editors (CBEs or ABEs) fused to catalytically dead Cas9 (dCas9) or nickase Cas9 (nCas9) are used to perform precise base editing without generating DSBs. In this chapter, we describe a detailed procedure to carry out single/multiple gene mutations and precise base editing in the Arabidopsis genome by using CRISPR/Cas9-based system. Specifically, the steps of target gene selection, sgRNA design, vector construction, transformation, and analysis of transgenic lines are described. The protocol is potentially adaptable to perform genome editing in other plant species such as rice.